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Quantitative & Systems Biology 251 (Manilay)

Introduction to PubMed

PubMed comprises over 30 million citations for biomedical literature from MEDLINE, life science journals, and online books, citations and abstracts dating back to 1966, selectively to 1865, and very selectively to the early 1800's. PubMed is the world's largest database of biomedical and health sciences literature. 

  • PubMed launched in 1996, is the interface used to access Medline, PubMed Central, plus additional materials (preprints, pre 1966 citations not yet updated to Medline, NCBI bookshelf, etc.). The earliest literature in PubMed dates back to the early 1800's.  
    • The name PubMed means for Public access to Medline.
  • MEDLINE is the National Library of Medicine (NLM) journal citation database; previously MEDLARS which launched in 1964. 
  • PubMed Central launched in 2000 as a free archive for full-text biomedical and life sciences journal articles.
  • MeSH, or Medical Subject Headings, are the National Library of Medicine's controlled vocabulary for indexing articles for MEDLINE/PubMed. Searching by using MeSH provide a consistent way to retrieve information that may use different terminology for the same concepts; locate MeSH using the MeSH database.

Find Articles by Topic

To perform a basic topic search, enter your topic keywords, and select search. For best results:

  • Be as specific as possible with your search terms.
  • Do NOT use punctuation, quotation marks, truncation, or operators like "and", "or". Let PubMed make these connections. 

For example, if you were interested in "yoga" and "mental health" and "prisons" search for:  

PubMed will map, or add synonyms and all relevant MeSH to your search. When a MeSH term is added to your search, all the MeSH subheadings and narrower terms are also included. 

To view the mappings, select Advanced under the search bar in the results screen. Note, subheadings and narrower terms  are not listed, but they  have been included in your search through a process called automatic explosion. 

Under the History and Search Details, click on the > icon in the Details column to view how PubMed interpreted your search. Here are the mappings for the above search. 

Advanced Search Builder

The Advanced Search Builder allows you to specify where you would like your search terms to appear by searching within specific fields, such as author, title/abstract, journal and many more. 

From the Advanced Search page, you can access your search history and search term details. The Advanced Search Builder also allows you to combine previous searches, and test out search terms by providing result numbers. 

Access the Advanced Search Builder from the Advanced link under the search bar on the homepage or the results page. 

To use the Advanced Search Builder: 

  • Specify the field you would like to search, enter your search terms and click Add to move your search into the Query Box.
  • Repeat to add additional search terms; change AND to OR or NOT as needed. 
  • When you have  finished adding your search terms, select Search, to search PubMed, or Add to History to save your search for the research session.

To run a previous search again, modify a previous search, or combine searches:

  • Scroll to the bottom of the Advanced Search page to the History and Search Details section. 
  • Click on the ... options in the Action Column to add the search to the Query Box.
  • Subsequent selections will provide you with AND and OR options for adding additional past searches. Add new search terms if desired.
  • History and Search Details are saved for a single research session; select Save to My NCBI to save a search for future use.
  • The Download option exports your search history to a CSV file. 

Searching with MeSH: Medical Subject Headings

MeSH are standardized terms that describe the main concepts of PubMed/MedLine articles. Searching with MeSH can increase the precision of your search by providing a consistent way to retrieve articles that may use different terminology or spelling variations. 

Note: new articles will not have MeSH terms; the indexing process may take up to a few weeks for newly ingested articles. 

Use the MeSH database to locate and build a search using MeSH.

  Access the Mesh Database from the PubMed homepage under the Explore menu.

To search the MeSH database:

  • Search for 1 concept at a time.
  • If you do not see a relevant MeSH in the results, search again with a synonym or related term.
  • Click on the MeSH term to view to the complete record​, subheadings, broader and narrower terms. 

Build a search from the results list or from the MeSH term record to specify subheadings.

  • Select the box next to the MeSH term or subheadings that you wish to search and click Add to Search Builder.
  • ​You may need to switch AND to OR, depending on how you would like to combine terms.
  • Repeat the above steps to add additional MeSH terms. When your search is ready, click Search PubMed.